On Mar 2, 2017, at 20:34, Craig James <cja...@emolecules.com> wrote: > Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states that > the "organic subset" are only allowed outside of brackets if they're in their > normal lowest-valence state. Actually, now that I read it, it's not well > written and has room for (mis)interpretation. The phrase that I think applies > in OpenSMILES is:
My understanding of Daylight SMILES is that when the explicit valence based on the bonds is higher than the maximum natural valence then the deduced hydrogen count is 0. For example, quoting http://www.daylight.com/meetings/summerschool98/course/dave/smiles-intro.html : > In practice, one chemist might represent nitromethane as C[N+](=O)[O-] with a > nitrogen of valence 3 in a charge-separated structure while another might > represent it as CN(=O)=O with a neutral 5-valent nitrogen. Which SMILES is > correct? Both are. On Mar 2, 2017, at 20:34, Craig James <cja...@emolecules.com> wrote: > If you can say, "It's obvious ...", and this is a feature everyone would > like, then the OpenSMILES spec could be changed. I think it should be changed. Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
